Contacts of the helix formed by residues 260 - 282 (chain A) in PDB entry 4A3K
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 3.5 45.7 - - + +
248A PRO* 3.8 20.2 + - - +
249A SER* 4.5 0.2 - - - +
258A GLY 3.8 0.8 + - - -
259A GLU* 1.3 78.8 + - - +
261A ASP* 1.3 81.6 + - - +
262A LEU* 2.9 13.2 + - - +
263A THR* 3.3 14.5 + - - +
264A PHE* 3.3 14.5 + - - -
323A LYS* 4.8 7.8 + - - +
328A ARG* 3.4 18.2 + - - -
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Residues in contact with ASP 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLU 4.1 0.2 + - - -
260A ASP* 1.3 79.1 + - - +
262A LEU* 1.4 55.8 + - + +
264A PHE* 3.2 12.7 + - - +
265A LYS* 3.0 28.6 + - - +
316A GLN* 4.3 10.1 - - - +
320A ARG* 3.1 33.1 + - - -
322A VAL* 3.3 17.5 - - - +
323A LYS* 2.8 64.5 + - + +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 5.2 4.9 - - + -
246A VAL* 4.2 14.6 - - + -
247A ARG* 3.8 15.5 - - + -
260A ASP* 2.9 10.2 + - - +
261A ASP* 1.4 76.2 - - + +
263A THR* 1.4 53.2 + - - +
265A LYS* 3.5 6.8 + - + +
266A LEU* 2.9 39.7 + - + +
303A TYR* 3.9 25.5 - - + +
322A VAL* 6.1 0.2 - - + -
323A LYS 4.1 18.2 - - - +
324A SER 5.0 0.4 - - - -
325A ILE* 3.8 36.3 - - + +
328A ARG* 3.5 34.8 - - - +
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 4.4 11.0 - - - +
53A LEU* 4.1 18.9 - - + +
54A ASN* 4.4 1.3 - - - +
247A ARG* 3.3 49.4 + - - +
259A GLU* 3.8 23.4 + - + +
260A ASP* 3.3 16.3 + - - +
262A LEU* 1.4 74.0 - - - +
264A PHE* 1.3 60.9 + - + +
266A LEU* 3.3 5.4 + - - +
267A ALA* 3.0 27.3 + - + +
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 5.7 1.6 - - - -
257A ARG* 5.5 7.9 - - - -
259A GLU* 3.4 46.9 - - + -
260A ASP 3.3 13.9 + - - -
261A ASP* 3.2 11.7 + - - +
263A THR* 1.3 75.9 - - + +
265A LYS* 1.4 59.8 + - - +
267A ALA* 3.0 12.1 + - + +
268A ASP* 2.9 32.9 + - - +
316A GLN* 4.1 25.6 - - - +
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Residues in contact with LYS 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A ASP 3.0 15.8 + - - +
262A LEU* 3.8 8.3 - - + +
264A PHE* 1.4 73.4 - - - +
266A LEU* 1.4 60.7 + - - +
268A ASP* 3.2 22.8 + - - +
269A ILE* 3.2 22.2 + - - +
299A HIS* 2.8 51.5 + - - +
302A THR* 3.3 24.3 + - - +
303A TYR* 3.6 33.7 - - + +
314A ALA* 3.9 14.1 - - + +
322A VAL* 3.8 32.5 - - + +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.8 10.1 - - + -
84A ILE* 5.5 4.7 - - + -
239A LEU* 4.7 8.1 - - + -
240A PRO 5.2 2.0 - - - +
241A VAL* 4.4 17.0 - - + -
242A PRO* 4.0 17.7 - - + -
247A ARG* 3.7 31.2 - - - +
262A LEU* 2.9 20.3 + - + +
263A THR* 3.5 6.1 - - - +
264A PHE 3.1 0.4 - - - -
265A LYS* 1.4 73.5 - - - +
267A ALA* 1.3 60.1 + - - +
269A ILE* 2.8 35.9 + - + +
270A LEU* 2.8 16.7 + - + +
303A TYR* 3.7 31.6 - - + +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PRO* 3.6 31.9 - - + +
53A LEU* 4.4 3.9 - - + +
263A THR* 3.0 12.6 + - + +
264A PHE* 3.0 14.2 + - + +
266A LEU* 1.3 74.3 - - - +
268A ASP* 1.3 51.8 + - - +
270A LEU* 3.3 9.9 - - - +
271A LYS* 2.8 47.1 + - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 2.9 15.2 + - - +
265A LYS* 3.2 35.8 + - - +
267A ALA* 1.3 76.3 - - - +
269A ILE* 1.4 51.7 + - - +
271A LYS* 3.3 19.1 + - - +
272A ALA* 2.8 35.7 + - - +
299A HIS* 3.5 29.4 + - + -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 4.8 7.6 - - + -
86A LEU* 4.4 6.1 - - + -
239A LEU* 4.0 17.7 - - + -
265A LYS 3.3 16.4 - - - +
266A LEU* 2.8 26.1 + - + +
268A ASP* 1.4 67.2 - - - +
270A LEU* 1.3 55.5 + - + +
272A ALA* 3.1 5.5 + - - +
273A ASN* 2.8 36.0 + - - +
296A LEU* 3.8 8.6 - - + +
299A HIS* 3.6 28.7 - - + +
300A VAL* 3.7 21.3 - - + -
303A TYR* 3.8 36.8 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.0 14.6 - - + +
36A ARG* 3.4 36.1 - - - +
37A PHE 3.7 3.4 - - - +
38A PRO* 3.6 24.0 - - + -
53A LEU* 5.1 4.3 - - + -
84A ILE* 3.7 40.4 - - + -
266A LEU* 2.8 13.3 + - + +
267A ALA* 3.3 14.6 - - - +
269A ILE* 1.3 77.5 - - + +
271A LYS* 1.3 57.4 + - - +
273A ASN* 3.0 5.9 + - + +
274A ILE* 2.9 43.3 + - + +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A PRO* 3.6 26.5 - - + -
267A ALA* 2.8 37.2 + - - +
268A ASP* 3.6 17.4 + - - +
270A LEU* 1.3 71.6 - - - +
272A ALA* 1.4 60.2 + - - +
273A ASN 3.3 0.3 + - - -
274A ILE* 3.3 10.3 + - + +
275A SER* 3.1 24.3 + - - -
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Residues in contact with ALA 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASP 2.8 20.7 + - - +
269A ILE* 3.5 5.2 - - - +
271A LYS* 1.4 72.3 - - - +
273A ASN* 1.4 57.4 - - - +
275A SER* 2.8 21.7 + - - -
276A LEU* 3.6 10.0 + - - +
292A ALA 4.0 7.3 - - - +
295A LEU* 3.9 20.9 - - + -
296A LEU* 4.0 18.9 - - - +
299A HIS* 3.7 19.3 - - + -
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Residues in contact with ASN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ILE* 3.4 21.7 - - + +
85A ASP 3.2 22.6 + - - -
86A LEU* 3.3 5.2 - - - -
87A ALA* 2.9 27.9 + - - +
269A ILE 2.8 12.2 + - - +
270A LEU* 3.3 10.1 - - - +
272A ALA* 1.4 75.0 - - - +
274A ILE* 1.4 68.8 + - + +
276A LEU* 3.3 5.4 + - - +
277A GLU* 3.0 26.2 + - - +
296A LEU* 3.7 21.1 - - + +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG 4.1 7.9 - - - +
38A PRO* 3.8 17.0 - - + -
270A LEU* 2.9 45.1 + - + +
271A LYS* 3.9 8.3 - - + +
273A ASN* 1.4 77.2 - - + +
275A SER* 1.4 63.0 + - - +
277A GLU* 3.6 17.0 + - - +
278A THR* 3.1 31.8 + - + +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LYS 3.1 12.8 + - - -
272A ALA* 2.8 19.0 + - - -
274A ILE* 1.4 74.5 - - - +
276A LEU* 1.4 72.1 + - - +
278A THR* 3.0 11.2 + - - -
279A LEU* 3.0 31.7 + - - +
292A ALA* 3.7 14.9 - - - +
295A LEU* 5.0 4.1 - - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.8 13.5 - - + -
88A LYS* 3.7 31.2 - - + -
272A ALA 3.7 9.9 - - - +
273A ASN* 3.3 8.6 + - - +
275A SER* 1.4 80.0 + - - +
277A GLU* 1.3 61.7 + - - +
279A LEU* 3.0 14.9 + - - +
280A GLU* 3.1 33.0 + - - +
289A ILE* 3.5 22.7 - - + +
292A ALA* 3.7 9.9 - - + +
293A GLU* 3.4 33.2 - - + +
296A LEU* 4.0 17.3 - - + -
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.9 19.0 - - + +
273A ASN* 3.0 19.8 + - - +
274A ILE* 3.8 14.2 - - - +
276A LEU* 1.3 75.4 - - - +
278A THR* 1.4 76.0 + - - +
280A GLU* 3.5 8.2 - - - +
281A HIS* 3.0 42.4 + - + +
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Residues in contact with THR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ILE* 3.1 23.0 + - + +
275A SER* 3.0 16.5 + - - -
277A GLU* 1.4 91.0 - - - +
279A LEU* 1.3 63.2 + - - +
281A HIS* 4.5 3.8 - - - -
282A ASN* 2.9 41.8 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A SER* 3.0 24.7 + - - +
276A LEU* 3.0 6.3 + - - +
278A THR* 1.3 81.2 - - - +
280A GLU* 1.3 57.4 + - - +
282A ASN* 3.0 22.5 - - - +
283A GLY 3.9 1.8 - - - +
284A ALA* 3.4 13.6 - - - -
285A PRO* 4.9 6.5 - - + -
288A ALA* 3.4 41.7 - - + +
289A ILE* 3.9 13.2 - - + +
292A ALA* 4.1 13.9 - - + -
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.5 22.7 - - - +
88A LYS* 3.7 20.8 - - - +
276A LEU* 3.1 40.3 + - - +
277A GLU* 3.5 14.1 - - - +
279A LEU* 1.3 75.2 - - - +
281A HIS* 1.4 63.3 + - - +
282A ASN 3.3 6.5 - - - +
284A ALA* 4.4 11.5 - - + +
289A ILE* 3.7 13.0 - - + +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU* 3.0 30.4 + - + +
278A THR* 4.1 5.6 - - + +
280A GLU* 1.4 75.5 - - - +
282A ASN* 1.4 72.4 + - - +
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A THR* 2.9 25.7 + - - +
279A LEU* 3.0 8.4 - - - +
280A GLU 3.3 5.7 - - - +
281A HIS* 1.4 96.4 + - - +
283A GLY* 1.3 57.6 + - - +
284A ALA* 2.7 17.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il